Merge pull request #261 from BrillouinMicroscopy/fix/noid/updates

chore: update dependencies and CI config
BrillouinMicroscopy · Jun 4, 2024 · 62b6cea · 62b6cea
2 parents fce710c + 75839db
commit 62b6cea
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Showing 16 changed files with 71 additions and 73 deletions.
diff --git a/.github/workflows/check_main_github.yml b/.github/workflows/check_main_github.yml
@@ -14,7 +14,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
         os: [macos-latest, ubuntu-latest, windows-latest]
         exclude:
           # 3.10 on macOS with shapely 1.8.0 is broken, but shapely >1.8.0 breaks the macOS DMG packages
@@ -35,7 +35,7 @@ jobs:
       if: runner.os == 'Linux'
       run: |
         sudo apt-get update
-        sudo apt-get install -y xvfb libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xinput0 libxcb-xfixes0 libegl1-mesa
+        sudo apt-get install -y xvfb libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xinput0 libxcb-xfixes0 libegl1-mesa libxcb-cursor0
         # start xvfb in the background
         sudo /usr/bin/Xvfb $DISPLAY -screen 0 1280x1024x24 &
     - name: Install dependencies for Mac and Linux
@@ -85,7 +85,7 @@ jobs:
       run: |
         bash ./macos_build_app.sh BMicro $(python -m bmicro --version)
     - name: Upload build artifacts
-      if: (runner.os == 'macOS' && matrix.python-version == '3.9')
+      if: (runner.os == 'macOS' && matrix.python-version == '3.12')
       uses: actions/upload-artifact@v3
       with:
         name: BMicro_macosx
@@ -102,7 +102,7 @@ jobs:
         python win_make_iss.py
         iscc /Q win_bmicro.iss
     - name: Upload build artifacts
-      if: (runner.os == 'windows' && matrix.python-version == '3.9')
+      if: (runner.os == 'windows' && matrix.python-version == '3.12')
       uses: actions/upload-artifact@v3
       with:
         name: BMicro

diff --git a/.github/workflows/check_stable_pypi.yml b/.github/workflows/check_stable_pypi.yml
@@ -14,7 +14,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
         os: [macos-latest, ubuntu-latest, windows-latest]
         exclude:
           # 3.10 on macOS with shapely 1.8.0 is broken, but shapely >1.8.0 breaks the macOS DMG packages
@@ -35,7 +35,7 @@ jobs:
       if: runner.os == 'Linux'
       run: |
         sudo apt-get update
-        sudo apt-get install -y xvfb libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xinput0 libxcb-xfixes0 libegl1-mesa libxcb-shape0
+        sudo apt-get install -y xvfb libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xinput0 libxcb-xfixes0 libegl1-mesa libxcb-shape0 libxcb-cursor0
         # start xvfb in the background
         sudo /usr/bin/Xvfb $DISPLAY -screen 0 1280x1024x24 &
     - name: Install dependencies
@@ -69,7 +69,7 @@ jobs:
       run: |
         bash ./macos_build_app.sh BMicro $(python -m bmicro --version)
     - name: Upload build artifacts
-      if: (runner.os == 'macOS' && matrix.python-version == '3.9')
+      if: (runner.os == 'macOS' && matrix.python-version == '3.12')
       uses: actions/upload-artifact@v3
       with:
         name: BMicro_macosx
@@ -86,7 +86,7 @@ jobs:
         python win_make_iss.py
         iscc /Q win_bmicro.iss
     - name: Upload build artifacts
-      if: (runner.os == 'windows' && matrix.python-version == '3.9')
+      if: (runner.os == 'windows' && matrix.python-version == '3.12')
       uses: actions/upload-artifact@v3
       with:
         name: BMicro

diff --git a/.github/workflows/deploy_github.yml b/.github/workflows/deploy_github.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ['3.9']
+        python-version: ['3.12']
         os: [macos-latest, windows-latest]
     steps:
     - uses: actions/checkout@v3
@@ -20,7 +20,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v3
       with:
-        python-version: 3.9
+        python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

diff --git a/.github/workflows/deploy_pypi.yml b/.github/workflows/deploy_pypi.yml
@@ -10,7 +10,7 @@ jobs:
     runs-on: macos-latest
     strategy:
       matrix:
-        python-version: ['3.9']
+        python-version: ['3.12']
 
     steps:
     - uses: actions/checkout@v3

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -2,12 +2,11 @@ version: 2
 formats:
  - pdf
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   tools:
-    python: "3.9"
+    python: "3.12"
 python:
   install:
     - requirements: docs/requirements.txt
     - method: pip
       path: .
-
diff --git a/bmicro/__main__.py b/bmicro/__main__.py
@@ -1,6 +1,6 @@
 def main():
     import os
-    import pkg_resources
+    from importlib import resources
     import sys
     import logging
 
@@ -13,9 +13,10 @@ def main():
     """
     app = QtWidgets.QApplication(sys.argv)
     # set window icon
-    imdir = pkg_resources.resource_filename("bmicro", "img")
-    icon_path = os.path.join(imdir, "icon.png")
-    app.setWindowIcon(QtGui.QIcon(icon_path))
+    ref = resources.files('bmicro') / 'img'
+    with resources.as_file(ref) as imdir:
+        icon_path = os.path.join(imdir, "icon.png")
+        app.setWindowIcon(QtGui.QIcon(icon_path))
 
     window = BMicro()
     window.show()

diff --git a/bmicro/gui/calibration/calibration_view.py b/bmicro/gui/calibration/calibration_view.py
@@ -1,4 +1,4 @@
-import pkg_resources
+from importlib import resources
 import logging
 
 from PyQt6 import QtWidgets, QtCore, uic
@@ -31,9 +31,9 @@ class CalibrationView(QtWidgets.QWidget):
     def __init__(self, *args, **kwargs):
         super(CalibrationView, self).__init__(*args, **kwargs)
 
-        ui_file = pkg_resources.resource_filename(
-            'bmicro.gui.calibration', 'calibration_view.ui')
-        uic.loadUi(ui_file, self)
+        ref = resources.files('bmicro.gui.calibration') / 'calibration_view.ui'
+        with resources.as_file(ref) as ui_file:
+            uic.loadUi(ui_file, self)
 
         self.mplcanvas = MplCanvas(self.image_widget,
                                    toolbar=('Home', 'Pan', 'Zoom'))
@@ -422,14 +422,15 @@ def find_peaks(self):
         self.refresh_plot()
 
     def show_options(self):
-        ui_file = pkg_resources.resource_filename(
-            'bmicro.gui.calibration', 'calibration_options.ui')
         self.options_dialog = QtWidgets.QDialog(
             self,
             QtCore.Qt.WindowType.WindowTitleHint |
             QtCore.Qt.WindowType.WindowCloseButtonHint
         )
-        uic.loadUi(ui_file, self.options_dialog)
+        ref = (resources.files('bmicro.gui.calibration') /
+               'calibration_options.ui')
+        with resources.as_file(ref) as ui_file:
+            uic.loadUi(ui_file, self.options_dialog)
         self.options_dialog.setWindowTitle('Calibration options')
         self.options_dialog.setWindowModality(
             QtCore.Qt.WindowModality.ApplicationModal)

diff --git a/bmicro/gui/data/data_view.py b/bmicro/gui/data/data_view.py
@@ -1,4 +1,4 @@
-import pkg_resources
+from importlib import resources
 import logging
 
 from PyQt6 import uic, QtWidgets
@@ -24,9 +24,9 @@ class DataView(QtWidgets.QWidget):
     def __init__(self, *args, **kwargs):
         super(DataView, self).__init__(*args, **kwargs)
 
-        ui_file = pkg_resources.resource_filename(
-            'bmicro.gui.data', 'data_view.ui')
-        uic.loadUi(ui_file, self)
+        ref = resources.files('bmicro.gui.data') / 'data_view.ui'
+        with resources.as_file(ref) as ui_file:
+            uic.loadUi(ui_file, self)
 
         self.mplcanvas = MplCanvas(self.image_preview_widget)
         self.preview = self.mplcanvas.get_figure().add_subplot(111)

diff --git a/bmicro/gui/evaluation/evaluation_view.py b/bmicro/gui/evaluation/evaluation_view.py
@@ -1,4 +1,4 @@
-import pkg_resources
+from importlib import resources
 import logging
 import numpy as np
 import matplotlib
@@ -43,9 +43,9 @@ class EvaluationView(QtWidgets.QWidget):
     def __init__(self, *args, **kwargs):
         super(EvaluationView, self).__init__(*args, **kwargs)
 
-        ui_file = pkg_resources.resource_filename(
-            'bmicro.gui.evaluation', 'evaluation_view.ui')
-        uic.loadUi(ui_file, self)
+        ref = resources.files('bmicro.gui.evaluation') / 'evaluation_view.ui'
+        with resources.as_file(ref) as ui_file:
+            uic.loadUi(ui_file, self)
 
         self.mplcanvas = MplCanvas(self.image_widget,
                                    toolbar=('Home', 'Pan', 'Zoom'))
@@ -314,16 +314,16 @@ def on_click_image(self, event):
 
     def open_image_spectrum(self):
         if self.image_spectrum_dialog is None:
-            ui_file = pkg_resources.resource_filename(
-                'bmicro.gui.evaluation', 'spectrum_view.ui')
             self.image_spectrum_dialog = QtWidgets.QDialog(
                 self,
                 QtCore.Qt.WindowType.WindowTitleHint |
                 QtCore.Qt.WindowType.WindowCloseButtonHint |
                 QtCore.Qt.WindowType.WindowMaximizeButtonHint |
                 QtCore.Qt.WindowType.WindowMinimizeButtonHint
             )
-            uic.loadUi(ui_file, self.image_spectrum_dialog)
+            ref = resources.files('bmicro.gui.evaluation') / 'spectrum_view.ui'
+            with resources.as_file(ref) as ui_file:
+                uic.loadUi(ui_file, self.image_spectrum_dialog)
             self.image_spectrum_dialog\
                 .setWindowTitle('Camera image & spectrum')
             self.image_spectrum_dialog.setWindowModality(
@@ -630,9 +630,9 @@ def refresh_plot(self):
                 # horizontal axis
                 image_map = data[tuple(dslice)]
                 image_map = np.rot90(image_map)
-                extent = np.nanmin(positions[idx[0]][tuple(dslice)]),\
-                    np.nanmax(positions[idx[0]][tuple(dslice)]),\
-                    np.nanmin(positions[idx[1]][tuple(dslice)]),\
+                extent = np.nanmin(positions[idx[0]][tuple(dslice)]), \
+                    np.nanmax(positions[idx[0]][tuple(dslice)]), \
+                    np.nanmin(positions[idx[1]][tuple(dslice)]), \
                     np.nanmax(positions[idx[1]][tuple(dslice)])
                 if isinstance(self.image_map, matplotlib.image.AxesImage):
                     self.image_map.set_data(image_map)

diff --git a/bmicro/gui/extraction/extraction_view.py b/bmicro/gui/extraction/extraction_view.py
@@ -1,4 +1,4 @@
-import pkg_resources
+from importlib import resources
 import logging
 
 from PyQt6 import QtWidgets, QtCore, uic
@@ -28,9 +28,9 @@ class ExtractionView(QtWidgets.QWidget):
     def __init__(self, *args, **kwargs):
         super(ExtractionView, self).__init__(*args, **kwargs)
 
-        ui_file = pkg_resources.resource_filename(
-            'bmicro.gui.extraction', 'extraction_view.ui')
-        uic.loadUi(ui_file, self)
+        ref = resources.files('bmicro.gui.extraction') / 'extraction_view.ui'
+        with resources.as_file(ref) as ui_file:
+            uic.loadUi(ui_file, self)
 
         self.mode = MODE_DEFAULT
         self.current_frame = 0

diff --git a/bmicro/gui/main.py b/bmicro/gui/main.py
@@ -1,5 +1,5 @@
 import pathlib
-import pkg_resources
+from importlib import resources
 import hashlib
 import signal
 import sys
@@ -8,15 +8,15 @@
 import numpy as np
 
 from PyQt6 import QtWidgets, uic, QtCore, QtGui
-from PyQt6.QtWidgets import QFileDialog, QMessageBox,\
+from PyQt6.QtWidgets import QFileDialog, QMessageBox, \
     QVBoxLayout, QWidget, QCheckBox, QHBoxLayout, QLabel, QLineEdit
 from PyQt6.QtCore import QSize
 
 from bmlab.session import Session
 from bmlab.file import is_source_file
 from bmlab.models.setup import AVAILABLE_SETUPS
 from bmlab.models import EvaluationModel
-from bmlab.controllers import PeakSelectionController, ExportController,\
+from bmlab.controllers import PeakSelectionController, ExportController, \
     EvaluationController
 
 from . import data
@@ -64,11 +64,14 @@ def __init__(self, *args, **kwargs):
 
         """ Initializes BMicro."""
         super(BMicro, self).__init__(*args, **kwargs)
-        ui_file = pkg_resources.resource_filename('bmicro.gui', 'main.ui')
-        uic.loadUi(ui_file, self)
+        ref = resources.files('bmicro.gui') / 'main.ui'
+        with resources.as_file(ref) as ui_file:
+            uic.loadUi(ui_file, self)
         QtCore.QCoreApplication.setApplicationName('BMicro')
 
-        self.imdir = pkg_resources.resource_filename("bmicro", "img")
+        ref = resources.files('bmicro') / 'img'
+        with resources.as_file(ref) as imdir:
+            self.imdir = imdir
 
         self.tabWidget.currentChanged.connect(self.update_ui)
 
@@ -200,14 +203,14 @@ def close_file(self):
         self.reset_ui()
 
     def on_action_export_file(self):
-        ui_file = pkg_resources.resource_filename(
-            'bmicro.gui', 'export_configuration.ui')
         self.export_dialog = QtWidgets.QDialog(
             self,
             QtCore.Qt.WindowType.WindowTitleHint |
             QtCore.Qt.WindowType.WindowCloseButtonHint
         )
-        uic.loadUi(ui_file, self.export_dialog)
+        ref = resources.files('bmicro.gui') / 'export_configuration.ui'
+        with resources.as_file(ref) as ui_file:
+            uic.loadUi(ui_file, self.export_dialog)
         self.export_dialog.setWindowTitle('Export configuration')
         self.export_dialog.setWindowModality(
             QtCore.Qt.WindowModality.ApplicationModal)
@@ -402,16 +405,16 @@ def on_action_about(self):
                                     f"BMicro {bmicroversion}", about_text)
 
     def on_action_batch_evaluation(self):
-        ui_file = pkg_resources.resource_filename(
-            'bmicro.gui', 'batch_evaluation.ui')
         self.batch_dialog = QtWidgets.QDialog(
             self,
             QtCore.Qt.WindowType.WindowTitleHint |
             QtCore.Qt.WindowType.WindowCloseButtonHint |
             QtCore.Qt.WindowType.WindowMaximizeButtonHint |
             QtCore.Qt.WindowType.WindowMinimizeButtonHint
         )
-        uic.loadUi(ui_file, self.batch_dialog)
+        ref = resources.files('bmicro.gui') / 'batch_evaluation.ui'
+        with resources.as_file(ref) as ui_file:
+            uic.loadUi(ui_file, self.batch_dialog)
         self.batch_dialog.setWindowTitle('Batch evaluation')
         self.batch_dialog.setWindowModality(
             QtCore.Qt.WindowModality.ApplicationModal)

diff --git a/bmicro/gui/peak_selection/peak_selection_view.py b/bmicro/gui/peak_selection/peak_selection_view.py
@@ -1,4 +1,4 @@
-import pkg_resources
+from importlib import resources
 import logging
 
 from PyQt6 import QtWidgets, uic
@@ -27,9 +27,10 @@ class PeakSelectionView(QtWidgets.QWidget):
     def __init__(self, *args, **kwargs):
         super(PeakSelectionView, self).__init__(*args, **kwargs)
 
-        ui_file = pkg_resources.resource_filename(
-            'bmicro.gui.peak_selection', 'peak_selection_view.ui')
-        uic.loadUi(ui_file, self)
+        ref = (resources.files('bmicro.gui.peak_selection') /
+               'peak_selection_view.ui')
+        with resources.as_file(ref) as ui_file:
+            uic.loadUi(ui_file, self)
 
         self.mplcanvas = MplCanvas(self.image_widget,
                                    toolbar=('Home', 'Pan', 'Zoom'))

diff --git a/build-recipes/hook-skimage.py b/build-recipes/hook-skimage.py
diff --git a/build-recipes/macos_build_requirements.txt b/build-recipes/macos_build_requirements.txt
@@ -1,7 +1,2 @@
 # Any additional requirements for building the application
-# There seems to be an issue with the scipy wheels for 1.8.0:
-# https://github.com/scipy/scipy/issues/15552
-scipy<1.8.0
 pyinstaller>=5.0
-shapely<1.8.1
-
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -4,6 +4,6 @@ ipython
 matplotlib
 numpy
 scipy
-sphinx==4.2.0
+sphinx
 sphinxcontrib.bibtex>=2.0
-sphinx_rtd_theme==1.0
+sphinx_rtd_theme